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A proposed marina for mega-yachts will no longer block some of the city’s most treasured views of the bay, thanks to a compromise between San Francisco and the America’s Cup.

Under the new plan announced Friday, organizers will give up their long-term development rights for piers 14 to 22 1/2 in exchange for the rights to develop Pier 54 in Mission Bay. At issue was the section of waterfront by Rincon Park, which, as Chronicle stories highlighted this summer, provides one of the few open water views of the bay along the Embarcadero.

But as city and cup officials celebrated, and key construction permits for the races sailed through the Port Commission, opponents were seeking to delay the world’s premier regatta.

Four environmental and neighborhood groups are appealing the event’s final environmental impact report. The eight-volume document, which by state law must be completed before construction begins, earned the Planning Commission’s unanimous approval Thursday.

The analysis fails to fully outline solutions to traffic jams, damage to plant life and other environmental problems, argue the Telegraph Hill Dwellers, San Francisco Tomorrow, the Golden Gate Audubon Society and Waterfront Watch.

Absent is “a complete and informationally adequate study of impacts on adjacent neighborhoods,” wrote attorney Keith Wagner of Lippe Gaffney Wagner LLP in the appeal.

The appeal is not necessarily a major setback to the regatta, which is scheduled to begin in eight months. It “was always built into the project schedule,” said Brad Benson, special projects manager for the port.

The next step comes in January, when the Board of Supervisors will consider the appeal. And if supervisors decide to let the project proceed, opponents could sue.

“If the appeal is not resolved successfully,” Benson said, “that would cause delays.”

The America’s Cup Village, the walkable area planned for Piers 27 to 29 by July 2013, could be stalled. Also at risk is a separate project to take shape on Pier 27 in February: the James R. Herman Cruise Terminal – an 88,000-square-foot facility for cruise ships – and the 2.5-acre Northeast Wharf Plaza.

On Friday, before the appeal was officially filed, the Port Commission approved several permits and procedural steps that opened the waterfront to both projects. Bauer’s Intelligent Transportation, a Pier 27 tenant that would be displaced by construction, got a new lease at Pier 50.

And city and cup officials stressed they had spent months listening to residents’ concerns. The prospect of losing the sight lines from Rincon Park, for instance, caused angry citizens to bombard port officials and the mayor with complaints.

“This will move the (planned) long-term marina from what is a passive area to a portion that is more a working waterfront,” said Monique Moyer, executive director of the port.

While Mayor Ed Lee hailed the new agreement as an example of how the city can work with both developers and concerned citizens to find a compromise, most of the give was from the organizers.

“The mayor called me into his office and suggested that (the pier 14 to 22 1/2 development) was off the table,” said Stephen Barclay, lead negotiator for the organizers.

The mayor admitted that the complaints were behind his decision to push hard for the exchange, saying that “the changes we’ve made were in response to people’s concerns.”

Barclay and the America’s Cup organizers “are learning what it’s like to do business with the city,” Lee said.